human_counts_dir <- "results/smrna_count/"
biotype_counts_files <- paste0 (
human_counts_dir,
sample_units$ sample_unit,
"_first_proper_pair_biotype_count.txt"
)
exogenous_counts_dir <- "results/exogenous_rna_count/"
exogenous_counts_files <- paste0 (
exogenous_counts_dir,
sample_units$ sample_unit,
"_idxstats.txt"
)
biotype_counts <- readr:: read_tsv (
biotype_counts_files[1 ],
comment = "#" ,
col_names = c ("biotype" , biotype_counts_files[1 ]),
col_types = "ci"
)
exogenous_counts <- read_tsv (
exogenous_counts_files[1 ],
col_names = c ("exogenous_rna" , exogenous_counts_files[1 ]),
col_types = "c-i-"
)
biotype_counts <- biotype_counts %>%
dplyr:: add_row (
biotype = "exogenous_rna" ,
"{biotype_counts_files[1]}" : = sum (exogenous_counts[[exogenous_counts_files[1 ]]])
)
for (i in 2 : length (biotype_counts_files)) {
biotype_sample <-
readr:: read_tsv (
biotype_counts_files[i],
comment = "#" ,
col_names = c ("biotype" , biotype_counts_files[i]),
col_types = "ci"
)
exogenous_counts_sample <-
readr:: read_tsv (
exogenous_counts_files[i],
col_names = c ("exogenous_rna" , exogenous_counts_files[i]),
col_types = "c-i-"
)
biotype_sample <- biotype_sample %>%
dplyr:: add_row (
biotype = "exogenous_rna" ,
"{biotype_counts_files[i]}" : =
sum (exogenous_counts_sample[[exogenous_counts_files[i]]])
)
biotype_counts <- biotype_counts %>%
dplyr:: full_join (biotype_sample, by = "biotype" )
}
biotype_counts <- biotype_counts %>%
rename_all (~ stringr:: str_replace_all (
., human_counts_dir, ""
)) %>%
rename_all (~ stringr:: str_replace_all (., "_first_proper_pair_biotype_count.txt" , "" )) %>%
tidyr:: pivot_longer (! biotype, names_to = "sample" , values_to = "count" )
biotype_counts